You can use the Cipher command to encrypt and decrypt data at the command line, in individual directories or in batches.

You can use the /d and /e switches with the Cipher command to encrypt or decrypt a directory, respectively. The syntax to encrypt a directory is cipher /e <directory name>. Note that these switches only work on directories-not on individual files. This is one of the most common mistakes made in using the tool, leading to complaints that "Cipher doesn’t work." No matter how many times you type cipher /e <filename>, your file won’t be encrypted. There is a clue in the message you get when you do this, shown below:

0 directorie(s) within 2 directorie(s) were encrypted.

As you might guess from this message, you need to be using the command with folder names, not file names.

Likewise, you can decrypt an encrypted directory using the command cipher /d<directory name>. Once again, it only works with directories.

You use the /s switch in conjunction with the /e or /d switch, and it makes it possible for you to perform the specified operation (encryption or decryption) on the subfolders within the folder you’re encrypting or decrypting. So if you have several layers of folders and want to quickly encrypt the entire tree, use the syntax cipher /e /s: <directory name>. You can decrypt the subdirectories within the directory in the same way, substituting /d for /e.

Note that you need to put a colon after the /s switch. The results of the command will name the subdirectories that have been encrypted or decrypted.